Mercurial > repos > devteam > emboss_5
comparison emboss_octanol.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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10:9b98d3d903c6 | 11:0e2484b6829b |
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1 <tool id="EMBOSS: octanol63" name="octanol" version="5.0.0"> | 1 <tool id="EMBOSS: octanol63" name="octanol" version="5.0.0.1"> |
2 <!-- graphics output with filename, no functional tests added --> | 2 <!-- graphics output with filename, no functional tests added --> |
3 <description>Displays protein hydropathy</description> | 3 <description>Displays protein hydropathy</description> |
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 4 <macros> |
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot | 5 <import>macros.xml</import> |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' octanol -sequence '$input1' -graph png -goutfile '$out_file1' -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot | |
6 -differenceplot $differenceplot -auto</command> | 9 -differenceplot $differenceplot -auto</command> |
7 <inputs> | 10 <inputs> |
8 <param format="data" name="input1" type="data"> | 11 <param name="input1" type="data" format="data" label="Sequences" /> |
9 <label>Sequences</label> | 12 <param name="width" type="integer" value="19" label="Window size" /> |
10 </param> | 13 <param name="octanolplot" type="select" label="Display the octanol plot"> |
11 <param name="width" type="text" value="19"> | |
12 <label>Window size</label> | |
13 </param> | |
14 <param name="octanolplot" type="select"> | |
15 <label>Display the octanol plot</label> | |
16 <option value="no">No</option> | 14 <option value="no">No</option> |
17 <option value="yes">Yes</option> | 15 <option value="yes">Yes</option> |
18 </param> | 16 </param> |
19 <param name="interfaceplot" type="select"> | 17 <param name="interfaceplot" type="select" label="Display the interface plot"> |
20 <label>Display the interface plot</label> | |
21 <option value="no">No</option> | 18 <option value="no">No</option> |
22 <option value="yes">Yes</option> | 19 <option value="yes">Yes</option> |
23 </param> | 20 </param> |
24 <param name="differenceplot" type="select"> | 21 <param name="differenceplot" type="select" label="Display the difference plot"> |
25 <label>Display the difference plot</label> | |
26 <option value="yes">Yes</option> | 22 <option value="yes">Yes</option> |
27 <option value="no">No</option> | 23 <option value="no">No</option> |
28 </param> | 24 </param> |
29 </inputs> | 25 </inputs> |
30 <outputs> | 26 <outputs> |
31 <data format="png" name="out_file1" /> | 27 <data name="out_file1" format="png" /> |
32 </outputs> | 28 </outputs> |
33 <help> | 29 <help> |
34 You can view the original documentation here_. | 30 You can view the original documentation here_. |
35 | |
36 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.html | |
37 | 31 |
38 ------ | 32 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/octanol.html |
39 | |
40 **Citation** | |
41 | |
42 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
43 | |
44 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
45 </help> | 33 </help> |
34 <expand macro="citations" /> | |
46 </tool> | 35 </tool> |